blender volume material has opaque surface
I noticed that all of the cubes had faces that were in exactly the same place, so I moved every cube around until none of them were touching. This could also be done by selecting each cube, setting the pivot point to individual origins and then scaling down slightly.

After that, it rendered as expected.



Just avoid having the faces of a mesh that has a volumetric shader applied in the same place. Intersections of the objects are fine though.



One more thing that I found is that you had many cubes that had an identical cube in the same place, so just avoid doing that. My render had some darker clouds because of that.